A new method has been developed to choose probable protein secondary conformations. Direct interatomic interaction energies are calculated to yield probabilities of various conformers. The side chain atoms are taken at fixed positions relative to the polypeptide backbone. Charges are assigned, for ionized groups, from pK values, and, for atoms in polar bonds, from small molecule dipole moments. Approximate energies of all possible helix and beta-strand segments are calculated. Several methods of selecting conformations have been investigated. In the most successful method, non-overlapping secondary regions are chosen sequentially; those with the most favorable energies are selected first.